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EP3790984A1 - Procédés destinés à une prédiction précoce, à une surveillance de réponse a un traitement, de récidive et de pronostic d'un cancer du sein - Google Patents

Procédés destinés à une prédiction précoce, à une surveillance de réponse a un traitement, de récidive et de pronostic d'un cancer du sein

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Publication number
EP3790984A1
EP3790984A1 EP19799344.7A EP19799344A EP3790984A1 EP 3790984 A1 EP3790984 A1 EP 3790984A1 EP 19799344 A EP19799344 A EP 19799344A EP 3790984 A1 EP3790984 A1 EP 3790984A1
Authority
EP
European Patent Office
Prior art keywords
methylation
gcm2
itpripl1
target
dna sequences
Prior art date
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Granted
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EP19799344.7A
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German (de)
English (en)
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EP3790984A4 (fr
EP3790984C0 (fr
EP3790984B1 (fr
Inventor
Ruo-kai LIN
Chin-sheng HUNG
Sheng-chao WANG
Yu-Mei CHUNG
Chih-Ming Su
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Eg Biomed Co Ltd
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Taipei Medical University TMU
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Publication of EP3790984C0 publication Critical patent/EP3790984C0/fr
Publication of EP3790984B1 publication Critical patent/EP3790984B1/fr
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

Definitions

  • the invention relates to gene biomarkers for prediction of risk or susceptibility of a breast cancer and/or prognosis and malignancy of a breast cancer. Particularly, the invention detects a breast cancer and predicts risk of a breast cancer or susceptibility to a breast cancer and/or prognosis and malignancy of the breast cancer based on methylation of gene biomarkers.
  • Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body and is a leading cause of deaths worldwide.
  • Methylated DNA has been studied as a potential class of biomarkers in the tissues of most tumor types.
  • DNA methyltransferases add a methyl group to DNA at cytosine-phosphate-guanine (CpG) island sites as an epigenetic control of gene expression.
  • CpG cytosine-phosphate-guanine
  • US 20080311570A1A provides a method for screening cancer that comprises the following steps: (1) providing a test specimen; (2) detecting the methylation state of the CpG sequence in at least one target gene within the genomic DNA of the test specimen, wherein the target genes consist of SOX1, PAX1, LMX1A, NKX6-1, WT1 and ONECUT1; and (3) determining whether there is cancer or cancerous pathological change in the specimen based on the presence or absence of the methylation state in the target gene.
  • WO 2016071477A1 relates to assessing the response of a cancer patient to a treatment by analyzing CpG methylation in the shox2 gene.
  • EP2828405B1 provides methods for detecting colorectal neoplasia by evaluating multiple gene markers in blood or plasma and stool. Summary of the Invention
  • the present disclosure discloses a set of novel epigenetic biomarkers for early prediction, treatment response, recurrence and prognosis monitoring of a breast cancer. Aberrant methylation of the genes can be detected in tumor tissues and plasma samples from cancer patients but not in normal healthy individuals.
  • the present disclosure also discloses primers and probes used herein.
  • the present disclosure discloses a method for detecting the methylation status in a human subject who is in a need of detection of a breast cancer, comprising (a) providing a biological sample, and (b) assaying methylation status of epigenetic biomarkers in target DNA sequences GCM2 and ITPRIPL1 or fragments thereof, wherein the presence of hypermethylation in the DNA sequences of the human subject relative to a methylation state of a control is indicative of a breast cancer.
  • the present disclosure discloses a method for detecting a predisposition to, or the incidence of, a breast cancer or predicting treatment response, prognosis or recurrence of a breast cancer in a human subject, comprising (a) providing a biological sample, and (b) assaying methylation status of epigenetic biomarkers in target DNA sequences GCM2 and ITPRIPL1 or fragments thereof, wherein the presence of hypermethylation in the DNA sequences of the human subject relative to a methylation state of a control is indicative of a predisposition to, or the incidence, poor treatment response, poor prognosis or recurrence of, the breast cancer.
  • a GCM2 methylation specific probe and a ITPRIPL1 methylation specific probe are used to assay the methylation level of the target GCM2 and ITPRIPL1 DNA sequences or fragments thereof and a control DNA sequence in the sample.
  • the present disclosure provides a method, comprising (a) providing a biological sample comprising GCM2 and ITPRIPL1 target DNA sequences or fragments thereof, and (b) assaying the methylation level of the target GCM2 and ITPRIPL1 DNA sequences or fragments thereof and a control DNA sequence in the sample using a GCM2 methylation specific probe and a ITPRIPL1 methylation specific probe, (c) measuring the relative methylation status of the target GCM2 and ITPRIPL1 DNA sequences or fragments thereof compared to a control DNA sequence to detect the presence of hypermethylated GCM2 and ITPRIPL1 , (d) identifying the subject as in need of breast cancer treatment when the target DNA sequences GCM2 and ITPRIPL1 DNA sequences or fragments thereof of the human subject are hypermethylated relative to methylation of a control DNA sequence in said subject.
  • the method can detect the methylation status in a human subject who is in need of detection of a breast cancer.
  • the present disclosure provides a method, comprising (a) providing a biological sample comprising GCM2 and ITPRIPL1 target DNA sequences or fragments thereof, and (b) assaying the methylation level of the target GCM2 and ITPRIPL1 DNA sequences or fragments thereof and a control DNA sequence in the sample using a GCM2 methylation specific probe and a ITPRIPL1 methylation specific probe, (c) measuring the relative methylation status of the target GCM2 and ITPRIPL1 DNA sequences or fragments thereof compared to a control DNA sequence to detect the presence of hypermethylated GCM2 and ITPRIPL1 , (d) identifying the subject as having a predisposition to, or the incidence, poor treatment response, or having poor prognosis or recurrence of, the breast cancer when the target DNA sequences GCM2 and ITRPIPL1 of the human subject are hypermethylated relative to a methylation state of a control DNA sequence in said subject.
  • a biological sample comprising GCM2 and ITPRIPL1
  • methylation in the DNA sequences GCM2 and ITPRIPL1 or fragments thereof described herein that is about 64% higher than that of the control indicates a breast cancer. In a further embodiment, methylation in the DNA sequences GCM2 and ITPRIPL1 or fragments thereof that is about 69% higher than that of the control indicates a breast cancer. In a further embodiment, methylation in the DNA sequences GCM2 and ITPRIPL1 or fragments that is about 69% and about 80% higher than that of the control respectively indicates a breast cancer.
  • a hypermethylation described herein is indicated when the methylation of the target DNA sequences in a human subject is at least 0.5, 1, 2 or 3 times higher than that in a control. In one embodiment, the hypermethylation is indicated when the methylation of the target DNA sequences in a human subject is at least 2 times higher than that in a control.
  • probes used in the methylation assay have a homology of about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or higher percent to a sequence(s) selected from the group consisting of SEQ ID NOs: l3 to 18.
  • the GCM2 methylation specific probe has a sequence with homology of at least 85% to SEQ ID NO: 15, and a ITPRIPL1 methylation specific probe has a sequence with homology of at least 85% to SEQ ID NO: 16.
  • the GCM2 methylation specific probe has a sequence of SEQ ID NO: 15 and a ITPRIPL1 methylation specific probe has a sequence of SEQ ID NO: 16.
  • the methods of the present disclosure further comprises a step of assaying the methylation level of the following one or more target DNA sequences or any of their combinations: ClorflM or a fragment thereof, ZNF177 or a fragment thereof and C8orf47 or a fragment thereof. Furthermore, the methylation level of RKL001 is further assayed.
  • a ClorflM methylation specific probe, a ZNF177 methylation specific probe, or a C8orf47 methylation specific probe or any of their combinations is further used to assay the methylation level of the following one or more target DNA sequences or any of their combinations: ClorflM or a fragment thereof, ZNF177 or a fragment thereof and C8orf47 or a fragment thereof.
  • the methylation specific probes of target ClorflM , ZNF177 and C8orf47 or fragments thereof have a sequence with homology of at least 85% to SEQ ID NOs: 17, 18 and 14, respectively.
  • the methylation specific probes of target ClorflM or a fragment thereof, ZNF177 or a fragment thereof and C8orf47 or a fragment thereof have a sequence of SEQ ID NOs: 17, 18 and 14, respectively.
  • DNA sequence has higher than about 75% of sensitivity and about 76% specificity for ClorflM , and higher than about 62% of sensitivity and about 82% specificity for ZNF177 , respectively.
  • the measure of the relative methylation status of the combination of target GCM2 and ITPRIPL1 or fragments thereof; target GCM2 , ITPRIPL1 and Clorfl 14 or fragments thereof; and GCM2 , ITPRIPLf ClorflM and ZNF177 or fragments thereof has higher than about 87% of sensitivity and about 96% specificity, higher than about 95% of sensitivity and about 72% specificity, higher than about 87% of sensitivity and about 96% specificity, respectively, compared to a control DNA sequence.
  • the measure futher comprises a step of measuring the specificity and sensitivity by a weighted sum score analysis.
  • the measure of the relative methylation status of the combination of target GCM2 , ITPRIPL1 and Clorfl or fragments thereof or target GCM2 , ITPRIPL1 , Clorfl and ZNF177 or fragments thereof has higher than about 87% of sensitivity and about 96% specificity and higher than about 91% of sensitivity and about 96% specificity, respectively.
  • an RKL001 methylation specific probe is further used to assay the methylation level of RKL001.
  • an RKL001 methylation specific probe has a sequence with homology of at least 85% to SEQ ID NO: 13. More preferably, an RKL001 methylation specific probe has a sequence with homology of SEQ ID NO: 13.
  • the methylation status is detected by polymerase chain reaction, nucleic acid sequencing (such as bisulfite sequencing or pyrosequencing), bisulfite conversion, mass spectrometry, methylation specific nuclease, mass-based separation, target capture or microarray.
  • nucleic acid sequencing such as bisulfite sequencing or pyrosequencing
  • bisulfite conversion such as bisulfite sequencing or pyrosequencing
  • mass spectrometry such as bisulfite sequencing or pyrosequencing
  • mass spectrometry such as bisulfite sequencing or pyrosequencing
  • mass spectrometry such as bisulfite sequencing or pyrosequencing
  • mass spectrometry such as bisulfite sequencing or pyrosequencing
  • mass spectrometry such as bisulfite sequencing or pyrosequencing
  • mass spectrometry such as bisulfite sequencing or pyrosequencing
  • mass spectrometry such as bisulfite sequencing or p
  • primers used in a polymerase chain reaction have a homology of about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or higher percent to a sequence(s) selected from the group consisting of SEQ ID NOs: 1 to 12.
  • primers having sequences of SEQ ID NOs: 5 to 8 or probes having sequences of SEQ ID Nos: 15 and 16 are used to detect or measure the methylation status of the target DNA sequences GCM2 and ITPRIPL1 or fragments thereof.
  • the present disclosure also provides a kit for detecting and/or characterizing the methylation profile of epigenetic biomarkers in target DNA sequences as described herein.
  • the kit can further comprise sodium bisulfite and adapters for whole target genes amplification, and polynucleotides (e.g., detectably-labeled polynucleotides) to quantify the presence of the converted methylated and or the converted unmethylated sequence of at least one cytosine from a DNA region of epigenetic biomarkers in target DNA sequences as described herein.
  • the kit can further comprise methylation sensing restriction enzymes for whole target sequence or genes amplification.
  • the kit further comprises one of more primers having sequences of SEQ ID NOs: 9 to 12 and 1 to 4 and/or one or more probes having sequences of SEQ ID Nos: 17, 18, 12 and 13 for assaying methylation status of epigenetic biomarkers in target DNA sequences GCM2 and ITPRIPL1 or fragments thereof in combination with one or more target DNA sequences C I orf 114 or a fragment thereof, ZNF177 or a fragment thereof, C8orf47 or a fragment thereof, and RKL0014 or any of combinations thereof.
  • the kit can be used for detecting and/or characterizing the methylation profile of epigenetic biomarkers in target DNA sequences GCM2 or a fragment thereof and ITPRIPL1 or a fragment thereof in combination with one or more target DNA sequences Cl orf 114 or a fragment thereof, ZNF177 or a fragment thereof, C8orf47 or a fragment thereof, and RKL0014 or any of combinations thereof.
  • the kit further comprises one of more primers having sequences of SEQ ID NOs: 9 to 12 and 1 to 4 and/or one or more probes having sequences of SEQ ID Nos: 17, 18, 12 and 13 to detect or measure the methylation status of the target DNA sequences.
  • the kit further comprises methylation sensing restriction enzymes for whole target sequence or genes amplification.
  • Figures 1 A to F show the heatmap for difference of methylation status of target nucleic acid and promoter, exon and gene body region of genes between tumor tissues and adjacent normal tissues, respectively (A: RKL001; B: C8orf47; C: GCM2; D: ClorflM; E: ITPRIPL1 ; F : ZNF177).
  • Figure 2 shows the difference in early detection of the methylation status of epigenetic biomarkers of target genes in plasma samples of healthy subjects and breast cancer patients.
  • FIG. 3 shows Receiver Operating Characteristic (ROC) Curve Analysis exhibiting the early detection of the methylation status of epigenetic biomarkers of target genes in breast cancer patients and healthy subjects.
  • GI GCM2 , ITPRIPL1 ;
  • GIC GCM2 , ITPRIPL1 , Clorfl ;
  • GICZ GCM2 , ITPRIPL1, Clorfl , ZNF177;
  • Figures 4 A to C show the treatment response through the methylation status of epigenetic biomarkers of target genes ClorflM (A), CA-153 (B) and CEA (C) in breast cancer patients before and after surgery.
  • Figure 5 shows poor prognosis in breast cancer patients based on the Kaplan-Meier curve of the methylation status of ITPRIPL1 gene.
  • AUC is an abbreviation for the area under a curve. In particular it refers to the area under a Receiver Operating Characteristic (ROC) curve.
  • the ROC curve is a plot of the true positive rate against the false positive rate for the different possible cut points of a diagnostic test. It shows the trade-off between sensitivity and specificity depending on the selected cut point (any increase in sensitivity will be accompanied by a decrease in specificity).
  • the area under an ROC curve (AUC) is a measure for the accuracy of a diagnostic test (the larger the area the better, optimum is 1, a random test would have a ROC curve lying on the diagonal with an area of 0.5; for reference: J. R Egan. Signal Detection Theory and ROC Analysis, Academic Press, New York, 1975).
  • biological sample refers to a sample of tissue, cells, or fluid isolated from a subject, including but not limited to, for example, blood, buffy coat, plasma, serum, blood cells (e.g., peripheral blood mononucleated cells (PBMCS), band cells, neutrophils, metamyelocytes, monocytes, or T cells), fecal matter, urine, bone marrow, bile, spinal fluid, lymph fluid, samples of the skin, external secretions of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, organs, biopsies and also samples of in vitro cell culture constituents, including, but not limited to, conditioned media resulting from the growth of cells and tissues in culture medium, e.g., recombinant cells, and cell components.
  • PBMCS peripheral blood mononucleated cells
  • band cells neutrophils, metamyelocytes, monocytes, or T cells
  • fecal matter e.g., urine, bone marrow,
  • biomarker refers to a nucleic acid molecule which is present in a sample taken from patients having human cancer as compared to a comparable sample taken from control subjects (e.g., a person with a negative diagnosis or undetectable cancer, normal or healthy subject).
  • the biomarker can be a nucleic acid, a fragment of a nucleic acid, a polynucleotide, or an oligonucleotide that can be detected and/or quantified.
  • Biomarkers include polynucleotides comprising nucleotide sequences from genes.
  • CpG island refers to stretches of DNA in a genome that are rich in GC relative to the rest of the genome. Typically, the GC content is 50% or greater in these regions, which extend over hundreds of base pairs and sometimes thousands. Often these regions mark the 5' ends of genes.
  • a "control amount" of a biomarker can be any amount or a range of amount which is to be compared against a test amount of a biomarker.
  • the term "early detection” of cancer refers to discovering the likelihood of cancer before metastasis. Preferably, it refers to discovering the likelihood of cancer before a morphological change in a sample tissue or cell is observed.
  • the terms“detect”,“detecting” or“detection” may describe either the general act of discovering or discerning or the specific observation of a detectably labeled composition.
  • the term "gene” refers to a nucleic acid (e.g., DNA) sequence that comprises coding sequences necessary for the production of a polypeptide, precursor, or RNA (e.g., non-coding RNAs such as ribosomal RNA, transfer RNA, splicosomal RNA, microRNA.).
  • RNA e.g., non-coding RNAs such as ribosomal RNA, transfer RNA, splicosomal RNA, microRNA.
  • a polypeptide or non-coding RNA can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragment polypeptide are retained.
  • a gene can include or exclude promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regions.
  • the term also encompasses the coding region of a structural gene and the sequences located adjacent to the coding region on both the 5' and 3' ends for a distance of about 1 kb or more on either end such that the gene corresponds in length to the full-length mRNA.
  • the term“gene” further includes both cDNA and genomic forms of a gene.
  • the term“homology” refers to a first sequence which shares a degree of sequence identity with a second sequence, but whose sequence is not identical to that of the second sequence.
  • a polynucleotide comprising the wild-type sequence of a mutant gene is homologous and non-identical to the sequence of the mutant gene.
  • the degree of homology between the two sequences is sufficient to allow homologous recombination therebetween, under appropriate stringent conditions.
  • nucleic acid and amino acid sequence identity include determining the nucleotide sequence of the mRNA for a gene and/or determining the amino acid sequence encoded thereby, and comparing these sequences to a second nucleotide or amino acid sequence. Genomic sequences can also be determined and compared in this fashion. In general, identity refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Two or more sequences (polynucleotide or amino acid) can be compared by determining their percent identity.
  • the percent identity of two sequences is the number of exact matches between two aligned sequences divided by the length of the shorter sequences and multiplied by 100.
  • the degree of sequence similarity between polynucleotides can be determined by hybridization of polynucleotides under conditions that allow formation of stable duplexes between homologous regions, followed by digestion with single-stranded- specific nuclease(s), and size determination of the digested fragments.
  • Two nucleic acid, or two polypeptide sequences are substantially homologous to each other when the sequences exhibit at least about 70%-75%, preferably 80%-82%, more preferably 85%-90%, even more preferably 92%, still more preferably 95%, and most preferably 98% sequence identity over a defined length of the molecules, as determined using the methods above.
  • substantially homologous also refers to sequences showing complete identity to a specified DNA or polypeptide sequence.
  • DNA sequences that are substantially homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. See , e.g., Sambrook et al., supra; Nucleic Acid Hybridization: A Practical Approach, editors B. D. Hames and S. J. Higgins, (1985) Oxford; Washington, D.C.; IRL Press).
  • treatment predictive factors are variables related to the response of an individual patient to a specific treatment, independent of prognosis.
  • methylation refers to the presence of a methyl group added by the action of a DNA methyl transferase enzyme to a cytosine base or bases in a region of nucleic acid, e.g., genomic DNA.
  • methylation state refers to the presence or absence of one or more methylated nucleotide bases in the nucleic acid molecule.
  • a nucleic acid molecule containing a methylated cytosine is considered methylated (i.e., the methylation state of the nucleic acid molecule is methylated).
  • a nucleic acid molecule that does not contain any methylated nucleotides is considered unmethylated.
  • hypom ethylation refers to the average methylation state corresponding to an increased presence of methylated nucleotide bases in the nucleic acid molecule at one or a plurality of CpG dinucleotides within a DNA sequence of a test DNA sample, relative to the amount of methylated nucleotide bases in the nucleic acid molecule found at corresponding CpG dinucleotides within a normal control DNA sample.
  • the term“hypomethylation” refers to the average methylation state corresponding to a decreased presence of methylated nucleotide bases in the nucleic acid molecule at one or a plurality of CpG dinucleotides within a DNA sequence of a test DNA sample, relative to the amount of methylated nucleotide bases in the nucleic acid molecule found at corresponding CpG dinucleotides within a normal control DNA sample.
  • tissue refers to a constitution or condition of the body which makes the tissues react in special ways to certain extrinsic stimuli and thus tends to make the individual more than usually susceptible to certain diseases.
  • target site or“target sequence” refers to a nucleic acid sequence that defines a portion of a nucleic acid to which a binding molecule will bind, provided sufficient conditions for binding exist.
  • the term "risk” refers to the estimated chance of getting a disease during a certain time period, such as within the next 10 years, or during the subject's lifetime.
  • prognosis as used herein generally refers to a prediction of the probable course and outcome of a clinical condition or disease. A prognosis of a patient is usually made by evaluating factors or symptoms of a disease that are indicative of a favorable or unfavorable course or outcome of the disease.
  • weight sum score refers to every possible alternative being rated by a score including all objectives, individually weighted to stress the importance of different objectives.
  • Cancer is characterized by an abnormal growth of a cell caused by one or more mutations or modifications of a gene leading to dysregulated balance of cell proliferation and cell death.
  • gene promoter CpG islands acquire abnormal hypermethylation, which results in transcriptional silencing that can be inherited by daughter cells following cell division.
  • DMA methyl ati on causing silencing in cancer typically occurs at multiple CpG sites in the CpG islands that are present in the promoters of protein coding genes.
  • Alterations of DNA methylation have been recognized as an important component of cancer development.
  • DNA methylation profiling provides higher clinical sensitivity and dynamic range compared to other cancer detections. Accordingly, the present disclosure provides a method and kit for early prediction, treatment response and prognosis or recurrence monitoring of breast cancer.
  • the methylation status of GCM2 and ITPRIPL1 target DNA sequences or fragments thereof in a biological sample are measured to detect a breast cancer or detect a predisposition to, or the incidence of, a breast cancer or predict treatment response, prognosis or recurrence of a breast cancer in a human subject.
  • the methylation status of Clorfl , ZNF177 and/or C8orf47 target DNA sequences or fragments thereof in a biological sample are measured to detect a breast cancer or detect a predisposition to, or the incidence of, a breast cancer or predict treatment response, prognosis or recurrence of a breast cancer in a human subject.
  • the methylation status of a nucleic acid sequence, RKL001, in human chromosome 19 is further measured.
  • GCM2 gene codes for glial cells missing homolog 2, which is thought to act as a binary switch between neuronal and glial cell determination.
  • the GCM protein and mammalian GCM homologs contain a conserved N-terminal GCM motif that has DNA-binding activity.
  • ITPRIPL1 gene codes from inositol l,4,5-trisphosphate receptor interacting protein like 1.
  • the ITPRIPL1 sequence and its function are known in the art such as described on website: https://www.genecards.org/cgi-bin/carddisp.pl7geneMTPRIPLl .
  • ZNF177 codes for zinc finger protein 111.
  • C8orf47 codes for glutamate rich protein 5.
  • RKL001 is a nucleic acid sequence in chromosome 19, which has the following sequence:
  • the methylation comprises a cytosine methylation site.
  • cytosine methylation comprises 5-methylcytosine (5-mCyt) and 5- hydroxymethylcytosine.
  • a cytosine methylation site occurs in a CpG dinucleotide motif.
  • a cytosine methylation site occurs in a CHG or CHH motif, in which is adenine, cytosine or thymine.
  • one or more CpG dinucleotide motif or CpG site forms a CpG island, a short DNA sequence rich in CpG dinucleotide.
  • CpG islands are typically, but not always, between about 0.2 to about 1 kb in length.
  • the methylation comprises CpG island methylation.
  • the methylation status is analyzed by a methylation specific enzymatic digest; bisulfite sequencing; an analysis selected from promoter methylation, CpG island methylation, MSP, HeavyMethyl, MethyLight, and Ms-SNuPE; and other methods relying on a detection of amplified DNA.
  • the term“MethyLightTM” refers to a fluorescence-based real- time PCR technique. MethylLight is described by Eads et ah, Cancer Res. 59:2302-2306, 1999, herein incorporated by reference.
  • the term“HeavyMethyl” assay refers to an assay wherein methylation specific blocking probes (also referred to herein as blockers) covering CpG positions between, or covered by the amplification primers enable methylation-specific selective amplification of a nucleic acid sample.
  • Ms-SNuPE refers to Methylati on-sensitive Single Nucleotide Primer Extension. MsSNuPE is described by Gonzalgo & Jones, Nucleic Acids Res. 25:2529-2531, 1997, herein incorporated by reference.
  • MSP refers to Methylation-specific PCR. MSP is described by Herman et al. Proc. Natl. Acad. Sci. USA 93:9821-9826, 1996, and by U.S. Pat. No. 5,786,146, each of which are herein incorporated by reference.
  • 5-methylcytosine has the same base pairing behavior as cytosine. Moreover, the epigenetic information carried by 5-methylcytosine is completely lost during, e.g., PCR amplification.
  • Bisulfite sequencing is a method for analyzing DNA for the presence of 5- methylcytosine is based upon the specific reaction of bisulfite with cytosine whereby, upon subsequent alkaline hydrolysis, cytosine is converted to uracil which corresponds to thymine in its base pairing behavior.
  • 5-methylcytosine remains unmodified under the
  • the original DNA is converted in such a manner that methylcytosine, which originally could not be distinguished from cytosine by its hybridization behavior, can be detected as the only remaining cytosine using molecular biological techniques, for example, by amplification and hybridization, or by sequencing.
  • the methylation status is detected by polymerase chain reaction, nucleic acid sequencing (such as bisulfite sequencing or pyrosequencing), bisulfite conversion, mass spectrometry, methylation specific nuclease, mass-based separation, target capture or microarray.
  • the methylation status is detected by using primers to amplify a methylated CpG of the target genes.
  • the detection of methylation is conducted by PCR, methylation specific PCR (MSP), real-time methylation specific PCR, quantitative methylation-specific PCR (QMSP), PCR using a methylated DNA-specific binding protein or quantitative PCR.
  • primer(s) that could amplify a methylated CpG of the genes described herein might be used.
  • the primer(s) comprises at least one or more CpG dinucleotide in a region which hybridizes to the methylated CpG of the genes.
  • the primer(s) for amplifying a methylated CpG of the genes comprise sequence(s) having a homology of about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or higher percent to sequence(s) selected from the group consisting of the following sequences.
  • Probe(s) capable of hybridizing with a methylated CpG of the genes described herein might be used.
  • the probe(s) capable of hybridizing with a methylated CpG of the genes comprise at least one or more CpG dinucleotide in a region which hybridizes to the methylated CpG of the genes.
  • probe(s) might comprise sequence(s) having a homology of about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or higher percent to sequence(s) selected from the group consisting of the following sequences.
  • the detection of the methylation status of the target genes comprises the presence of hypermethylation in the genes relative to a normal state of the target genes.
  • the biological sample is a tissue, cell, blood, urine, serum or plasma from a patient suspected of having breast cancer or a subject to be detected.
  • a patient suspected of having cancer refers to an individual who has received an initial diagnosis (e.g ., a CT scan showing a mass or increased biomarker level) but for whom the stage of cancer or presence or absence of methylated genes indicative of cancer is not known.
  • the term further includes people who once had cancer (e.g., an individual in remission).
  • a detection test to correctly predict status is measured as the sensitivity of the assay, the specificity of the assay or the area under a receiver operated characteristic (ROC) curve (AUC).
  • ROC receiver operated characteristic
  • a weighted sum score is measured to determine the methylation status in the nucleic acid sequence and genes as an indicator.
  • the weighted sum model is the best known and simplest multi-criteria decision analysis (MCDA)/multi-criteria decision making method for evaluating a number of alternatives in terms of a number of decision criteria.
  • the weighted sum score analysis shows the combination of GCM2, ITPRIPLJ Clorfl 14 and ZNF177 shows a sensitivity higher than about 91% and a specificity higher than about 96% than the control.
  • one or more of the biomarkers disclosed herein show a statistical difference in different samples of at least p ⁇ 0.05. Detection tests that use these biomarkers may show an AUC of at least 0.9.
  • the hypermethylation status of the epigenetic biomarkers in DNA sequences described herein correlates with a "poor" prognosis or the likelihood that a subject will likely respond unfavorably to a drug or set of drugs, leading to a progression of a cancer and/or to refractory of one or more therapeutic agents.
  • a "poor" prognosis refers to the likelihood that a subject will not respond to a drug or set of drugs, leading to a progression of a cancer.
  • a “poor” prognosis refers to the survival of a subject of from less than 5 years to less than 1 month.
  • a “poor” prognosis refers to the survival of a subject in which the survival of the subject upon treatment is from less than 5 years to less than 1 month. In some instances, a “poor” prognosis further refers to the likelihood that a subject will develop a refractory cancer toward one or more drugs. [ 0077 ] In some embodiments, the present disclosure provides a kit for detecting and/or characterizing the methylation profile of the target DNA sequences l9described herein.
  • the target DNA sequences comprises the combination selected from the group consisting of: GCM2 and ITPRIPL1 ; GCM2 , ITPRIPL1 and ClorflM; GCM2 , ITPRIPL1, ClorflM and ZNF177 GCM2 , ITPRIPL1 , ClorflM , ZNF177 and RKL1001; and GCM2 , ITPRIPL1 , ClorflM and ZNF177 , RKL1001 and C8orf47.
  • the kit comprises a plurality of primers or probes to detect or measure the methylation status/levels of one or more target genes.
  • kits comprise, in some instances, at least one polynucleotide that hybridizes to at least one of the methylation biomarker sequences described herein and at least one reagent for detection of gene methylation.
  • Reagents for detection of methylation include, e.g., sodium bisulfate, polynucleotides designed to hybridize to sequence that is the product of a marker sequence if the marker sequence is not methylated (e.g., containing at least one C-U conversion), and/or a methylation-sensitive or methylation-dependent restriction enzyme.
  • kits provide solid supports in the form of an assay apparatus that is adapted to use in the assay.
  • the kits further comprise detectable labels, optionally linked to a polynucleotide, e.g., a probe, in the kit.
  • the kit further comprises a process unit to obtain a weighted sum score as described herein.
  • kits comprise sufficient primers to amplify the target DNA sequences described herein, and optionally include detectably-labeled polynucleotides capable of hybridizing to each amplified DNA region or portion thereof.
  • the kits further can comprise a methylation-dependent or methylation sensitive restriction enzyme and/or sodium bisulfite.
  • kits comprise sodium bisulfite, primers and adapters for whole target genes amplification, and polynucleotides (e.g., detectably-labeled polynucleotides) to quantify the presence of the converted methylated and or the converted unmethylated sequence of at least one cytosine from a DNA region of an epigenetic biomarker described herein.
  • polynucleotides e.g., detectably-labeled polynucleotides
  • kits comprise methylation sensing restriction enzymes, primers and adapters for whole target genes amplification, and polynucleotides to quantify the number of copies of at least a portion of a DNA region of an epigenetic marker described herein.
  • the kits comprise a methylation binding moiety and one or more polynucleotides to quantify the number of copies of at least a portion of a DNA region of a marker described herein.
  • any of the terms “comprising”,“consisting essentially of’, and“consisting of’ may be replaced with either of the other two terms in the specification.
  • the terms“comprising”,“including”, containing”, etc. are to be read expansively and without limitation.
  • the methods and processes illustratively described herein suitably may be practiced in differing orders of steps, and that they are not necessarily restricted to the orders of steps indicated herein or in the claims. It is also that as used herein and in the appended claims, the singular forms“a,”“an,” and“the” include plural reference unless the context clearly dictates otherwise.
  • the b value for Illumina Methylation 450K array-based data was generated from The Cancer Genome Atlas (TCGA) Research Network. The target nucleic acid and genes were selected when b value from normal tissues is less than 0.15; D b value (the value of Tumor subtracts that of normal tissues) is higher than 0.3. The D b value of GCM2 , ITPRIPLf ClorflM and ZNF177 , RKL1001 and C8orf47 is much higher than 0.3.
  • Genomic DNA from matched pairs of primary tumors and adjacent breast tissues from the same patient from breast cancer patients were extracted and followed by bisulfite conversion.
  • the methylation specific real-time PCR (qMSP) was used in detection of DNA methylation analyses in breast tumor tissues and adjacent normal tissues.
  • the ACTB gene was used as a reference gene.
  • the circulating cell-free DNA was extracted from plasma. Briefly, 3.5 mL of plasma was isolated immediately from 10 mL of peripheral blood. After circulating cell-free DNA (cfDNA) was extracted from plasma that obtained from 24 breast cancer patients and 25 healthy subjects, cfDNA was performed by bisulfite conversion. Probe-based methylation specific real- time PCR (qMSP) was used for cfDNA methylation analyses. The early prediction by GCM2 , ITPRIPL1 , Clorfl 14 and ZNF177 revealed 91.7% sensitivity and 96.0% specificity (AUC: 0.954).
  • Figure 2 shows the difference in early detection of the methylation status of epigenetic biomarkers of target genes in plasma samples of healthy subjects and breast cancer patients.
  • Receiver Operating Characteristic (ROC) Curve Analysis as shown in Figure 3 indicates the early detection of the methylation status of epigenetic biomarkers of target genes in breast cancer patients and healthy subjects.

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Abstract

La présente invention concerne un ensemble de nouveaux biomarqueurs épigénétiques destinés à une prédiction précoce, à une surveillance de réponse à un traitement, de récidive et de pronostic d'un cancer du sein. La méthylation aberrante des gènes peut être détectée dans des tissus tumoraux et des échantillons de plasma provenant de patient(e)s atteint(e)s d'un cancer du sein mais pas chez un individu sain normal. La présente invention concerne également des amorces et des sondes utilisées dans l'invention.
EP19799344.7A 2018-05-08 2019-05-08 Procédés destinés à une prédiction précoce, à une surveillance de réponse a un traitement, de récidive et de pronostic d'un cancer du sein Active EP3790984B1 (fr)

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JP7649437B2 (ja) 2025-03-21
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AU2019265619B2 (en) 2025-05-08
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US20210189500A1 (en) 2021-06-24
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EP3790984B1 (fr) 2023-11-22
WO2019217537A1 (fr) 2019-11-14
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